Complete Genome Sequence of Kosakonia Oryzae Type Strain Ola 51T Yuanyuan Li1†, Shuying Li1†, Mingyue Chen1, Guixiang Peng2, Zhiyuan Tan3* and Qianli An1*
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Li et al. Standards in Genomic Sciences (2017) 12:28 DOI 10.1186/s40793-017-0240-8 SHORT GENOME REPORT Open Access Complete genome sequence of Kosakonia oryzae type strain Ola 51T Yuanyuan Li1†, Shuying Li1†, Mingyue Chen1, Guixiang Peng2, Zhiyuan Tan3* and Qianli An1* Abstract Strain Ola 51T (=LMG 24251T = CGMCC 1.7012T) is the type strain of the species Kosakonia oryzae and was isolated from surface-sterilized roots of the wild rice species Oryza latifolia grown in Guangdong, China. Here we summarize the features of the strain Ola 51T and describe its complete genome sequence. The genome contains one circular chromosome of 5,303,342 nucleotides with 54.01% GC content, 4773 protein-coding genes, 16 rRNA genes, 76 tRNA genes, 13 ncRNA genes, 48 pseudo genes, and 1 CRISPR array. Keywords: Endophyte, Kosakonia, Nitrogen fixation, Plant growth-promoting bacteria Introduction the genetic information to study its plant growth- Enterobacter cowanii [1], E. radicincitans [2], E. oryzae promoting potential and its plant-associated life style. [3], E. arachidis [4], E. sacchari [5], E. oryziphilus [6, 7], and E. oryzendophyticus [6, 7] have been transferred into the novel genus Kosakonia of the family “Enterobacteria- Organism information ceae” [8–10]. A novel species “Kosakonia pseudosac- Classification and features chari” [11] closely related to K. sacchari was recently K. oryzae strain Ola 51T is a Gram-negative, non-spore- proposed. With the exception of the type species K. cow- forming, motile rod with peritrichous flagella (Fig. 1). It anii, which was originally obtained from clinical samples grows aerobically but reduces N2 to NH3 at a low pO2. [1], the other members of the genus Kosakonia are It forms circular, convex, smooth colonies with entire nitrogen-fixing bacteria associated with plants [2–6, 11] margins on nutrient agar [3, 8]. It grows best around and commonly occur in the nitrogen-fixing bacterial 30 °C and pH 7 (Table 1) [3]. K. oryzae Ola 51T has the community of some non-legume crops, such as rice [6] typical biochemical phenotypes of the genus Kosakonia: and sugarcane [12]. Some nitrogen-fixing Kosakonia positive for acetoin production (Voges-Proskauer test) strains are able to promote crop growth [12–14]. while negative for indole production; positive for β- Strain Ola 51T (=LMG 24251T=CGMCC 1.7012T)is galactosidase and arginine dihydrolase while negative for the type strain of the species Kosakonia oryzae and was lysine decarboxylase; positive for oxidation of arabinose, isolated from surface-sterilized roots of the wild rice spe- cellobiose, citrate, fructose, galactose, gluconate, glucose, cies Oryza latifolia grown in Guangdong, China [3]. glycerol, lactose, malate, maltose, mannitol, mannose, Here we present the summary of the features of the K. sorbitol, sucrose and trehalose (Table 1) [3, 8]. oryzae type strain Ola 51T and its complete genome se- The 16S rRNA gene sequence of K. oryzae Ola 51T quence, which provides a reference for resolving the was deposited in GenBank under the accession number phylogeny and taxonomy of closely related strains and EF488759 [3]. A phylogenetic analysis of the 16S rRNA gene sequences from the strains belonging to the genus Kosakonia and Escherichia coli ATCC11775T (the type * Correspondence: [email protected]; [email protected] strain of the type species of the type genus of the family T †Equal contributors Enterobacteriaceae) showed that K. oryzae Ola 51 is 3College of Agriculture, South China Agricultural University, Guangzhou most closely related to the strains belonging to the spe- 510642, China K. radicincitans – 1State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang cies (Fig. 2) [3, 8 11]. University, Hangzhou, China Full list of author information is available at the end of the article © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Li et al. Standards in Genomic Sciences (2017) 12:28 Page 2 of 7 Table 1 Classification and general features of Kosakonia oryzae strain Ola 51T according to the MIGS recommendations [15] MIGS ID Property Term Evidence codea Classification Domain Bacteria TAS [34] Phylum Proteobacteria TAS [35] Class Gammaproteobacteria TAS [36, 37] Order “Enterobacteriales” TAS [38] Family Enterobacteriaceae TAS [39, 40] Genus Kosakonia TAS [8] Species Kosakonia oryzae TAS [3, 8] Type strain: Ola 51T TAS [3] Gram stain Negative TAS [3] Cell shape Rod TAS [3] Motility Motile TAS [3] Sporulation Non-sporulating TAS [3] Temperature 10–40 °C TAS [3] Fig. 1 Cell morphology of the Kosakonia oryzae type strain Ola 51T.The range bacterium was stained by uranyl acetate and observed by a transmission Optimum 28–37 °C TAS [3] electron microscope temperature pH range; 3.5–10; 6.0–8.0 TAS [3] Optimum Arabinose, cellobiose, Chemotaxonomic data Carbon source citrate, fructose, galactose, TAS [3, 8] Whole-cell fatty acids were extracted from cells grown gluconate, glucose, glycerol, aerobically at 28 °C for 24 h on the TSA medium lactose, malate, maltose, mannitol, mannose, sorbitol, according to the recommendations of the Microbial sucrose & trehalose Identification System (MIDI Inc., Delaware USA). The MIGS-6 Habitat Plants TAS [3] whole-cell fatty acid composition was determined using MIGS-6.3 Salinity 0 – 5% NaCl (w/v) TAS [3] a 6890 N gas chromatograph (Agilent Technologies, Santa Clara, USA) and the peaks of the profiles were MIGS-22 Oxygen Facultatively anaerobic TAS [3] requirement identified using the TSBA50 identification library version K. oryzae T MIGS-15 Biotic Free-living, endophytic TAS [3] 5.0 (MIDI). Ola 51 shows the typical cell fatty relationship acid profile of the genus Kosakonia [8]. The major fatty MIGS-14 Pathogenicity Not reported acids are C16:0,C18:1 ω7c,C16:1 ω7c/15:0 iso 2OH,C17:0 cyclo and C [8, 11]. MIGS-4 Geographic Guangzhou, Guangdong, TAS [3] 14:0 3OH/16:1 iso I location China MIGS-5 Sample September 12, 2005 TAS [3] Genome sequencing information collection Genome project history K. oryzae T MIGS-4.1 Latitude 23.1634171311 °N NAS Ola 51 was selected for sequencing based on its MIGS-4.2 taxonomic significance. The genome sequence is deposited Longitude 113.3534469581°E NAS in GenBank under the accession number CP014007. A MIGS-4.3 Depth 0.2 – 0.3 m below the TAS [3] summary of the genome sequencing project information surface and its association with MIGS version 2.0 [15] is shown in MIGS-4.4 Altitude 20 m NAS Table 2. a Evidence codes – IDA: Inferred from Direct Assay; TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Au- thor Statement (i.e., not directly observed for the living, isolated sample, but Growth conditions and genomic DNA preparation based on a generally accepted property for the species, or anecdotal evi- K. oryzae Ola 51T was grown aerobically in liquid Luria- dence). These evidence codes are from the Gene Ontology project [41] Bertani medium at 30 °C until early stationary phase. The genome DNA was extracted from the cells by using Genome sequencing and assembly a TIANamp bacterial DNA kit (Tiangen Biotech, Beijing, The genomic DNA of K. oryzae Ola 51T was con- China). DNA quality (OD260/OD280 = 1.8) and quantity structed into 8 – 11 kb insert libraries and sequenced (22 μg) were determined with a Nanodrop spectrometer using PacBio SMRT sequencing technology [16] at the (Thermo Scientific, Wilmington, USA). Duke University Genome Sequencing & Analysis Core Li et al. Standards in Genomic Sciences (2017) 12:28 Page 3 of 7 Fig. 2 Phylogenetic tree based on the 16S rRNA gene sequences showing the phylogenetic position of the Kosakonia oryzae type strain Ola 51T (●) and other strains belonging to the genus Kosakonia. The sequences were aligned using the SINA (SILVA Incremental Aligner) Alignment Service [42] and were constructed to the phylogenetic tree with the neighbor-joining algorithm and the Kimura 2-parameter model integrated in the MEGA 5.2 program [43]. Bootstrap values (>50%) of 1,000 tests are shown at the nodes. The tree was rooted on the outgroup Escherichia coli ATCC 11775T. The GenBank accession numbers of the sequences are indicated in brackets; * indicates the accession number of a contig of the whole genome sequence. The scale bar indicates 0.1% substitutions per site Resource. Sequencing was run on two SMRT cells Genome annotation and resulted in 124,997 high-quality filtered reads Automated genome annotation was done using the with an average length of 8,260 bp. High-quality reads NCBI Prokaryotic Genome Annotation Pipeline [17]. were assembled by the RS_HGAP_Assembly.3 in the Functional annotations were done by searching against SMRT analysis v2.3.0. The final assembly produced the KEGG [18], InterPro [19], and COG [20] databases. 128-fold coverage of the genome. Genes with signal peptides were predicted using SignalP [21]. Genes with transmembrane helices were predicted using TMHMM [22]. Table 2 Genome sequencing project information for Kosakonia T Genome properties oryzae strain Ola 51 The genome of K. oryzae Ola 51T contains one circular MIGS ID Property Term chromosome (Fig. 3). The chromosome contains MIGS 31 Finishing quality Finished 5,303,342 nucleotides with 54.0% G + C content. The MIGS-28 Libraries used PacBio 8 –11 Kb library genome contains 4,926 predicted genes, 4773 protein- MIGS 29 Sequencing platforms PacBio RS II coding genes, 105 RNA genes (16 rRNA genes, 76 tRNA MIGS Fold coverage PacBio 128 × genes, and 13 ncRNA genes), 48 pseudo genes, and 1 31.2 CRISPR repeats.